Minor factions.
First, instead of taking the last one out, put them all back in.
Second, Put their Sov inside of the freaking city.
Third, Make the City un-raze-able.
Fourth, instead of it being a "city" make it a special spot like a city that can produce troops and sell special items.
Fifth, these troops are not designed, they are like darklings or dragons, they are what they are, but they reflect the minor civ. The Orekeepers have a special armor they make. So the troops could be just "Orekeepers" and they could have longswords and Pressed iron Armor.
You could still have diplomacy with them, marry, or whatever. If you conquered them, you can't, as those people are dead, but can still sell the special items and make the special troops. If you ally with them, or take them over through influence, then you can still use diplomacy.
Sixth, make their city produce the crap they need to build troops. So they might not have to build any thing, but their special city produces metal, resources, etc so they can. They could produce troops, but can't declare war, they as minor nations can only have war declared on them, OR go to war to defend an ally.